Are there deep networks that can differentiate object class from individual object?
In this case, you have an ontology and want to learn the ontology. There are many researches in this topic that you can find. However, the data could be the most challenging part. Some of the researches: 


Ontology learning for the Semantic Web 
Ontology Learning


Also, as these are some frameworks to ontology learning, you can use deep networks such as RNN‌ to learn the task.